When Running Demo Snakemake Crashes

[JooshK]

Description of the bug

I created a conda environment and ran the demo using 4 cores, at step 13 the an error in rule asses_pdbs occurred as as a python AttributeError of the module arcadia pycolor, missing an atribute 'Gradients'. Thanks in advance for your help:

Command used and terminal output

$ snakemake --snakefile Snakefile --configfile demo/search-mode/config_actin.yml --use-conda --cores 4
...
Activating conda environment: .snakemake/conda/0edc9d41bbd7c35062b5ad31e774a114_
Traceback (most recent call last):
  File "/home/oconnorlab/joshuak/protein_cartography/ProteinCartography/ProteinCartography/assess_pdbs.py", line 10, in <module>
    from color_utils import RESIDUE_CONFIDENCE_COLORS
  File "/home/oconnorlab/joshuak/protein_cartography/ProteinCartography/ProteinCartography/color_utils.py", line 7, in <module>
    arcadia_viridis = apc.Gradients["arcadia:viridis"].grad_nested_list
AttributeError: module 'arcadia_pycolor' has no attribute 'Gradients'. Did you mean: 'gradients'?

Relevant files

2024-07-12T121623.218462.snakemake.log

System information

Desktop, Ubuntu Linux 22.04 Snakemake: 7.25.3 Version v0.5

[mezarque]

Hi there, thanks for letting us know about this bug! We'll work on resolving this. If you'd like to quickly fix the issue, you should be able to resolve it by replacing the line in envs/plotting.yml below:

      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git#egg=arcadia_pycolor"

with this line:

      - "git+https://github.com/Arcadia-Science/arcadia-pycolor.git@245ad0c#egg=arcadia_pycolor"

[keithchev]

This should be fixed by #89. Please let us know if you encounter any other problems!